The Doctor's children included thirteen children with his wife "Patience". Susan Foreman's father was the eldest of these children. (PROSE: Cold Fusion).
Miranda Dawkins was the daughter of the Emperor, a future incarnation of the Doctor, who was later adopted by the Eighth Doctor. (PROSE: Father Time)
Jenny was the daughter of the Tenth Doctor who was artificially created from his DNA by a progenation machine. (TV: The Doctor's Daughter)
The Sapling was a sapling of the Planting who was infused with some of the memories of the Eleventh Doctor and Alice Obiefune as his "progenitors". (COMIC: The Scream, et al)